State religions were cast aside during the Ade of Reason as they were seen as bad for government. Philosophers came to see the teachings of the church as backwards and felt their government owed no loyalty to it. The populace at large however did not demand secular government. In the case of India, Muslims planned to break away from the nation rather than be ruled by a Pro-Hindu government. As I remember, I don't think they believed a truly secular government could be made in India and even if it could, they would still rather live under Islamic law. Pakistan did break away, however, secular government still dominated in India because of the teachings to the Age of Reason which have become popularly accepted as laws of good government. The reason for this being the resounding success of secular governments in the past. No one ever demanded a secular government. Everyone just keeps demanding that their religion should be the state religion. I'm not convinced that the populace at large honestly believes secular government is good, I keep hearing they talk about how their religion really should run the government. However, secular and liberal governments do have some inherit traits which make them desirable, but they do not cause unhappiness in religious states (just mildly bad relations).
It;'s easy to look around today and say that all the best governments are secular, but 500 years ago, all the best governments were monarchical and feudalistic, and 2000 years ago all the best governments were imperialistic. To be fair (and objective), RoM should not acknowledge any civic as being superior do another in the minds of the entire populace. It is understandable that people of non-state religions would not like a country with a state religion, but other countries being liberal or secular does not affect the perception at large.
That brings up another issue. Ive noticed several civics are pretty muc useless or become obsolete over time. I love state church, but that -20% science really puts your government at a major disadvantage. Also, divine cult is completely useless, as are nobility, despotism, marxism, ad so forth. I really miss that ridiculous feature of Civ4 where communism almost always solves all your economic problems.